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feat: add parallel distance matrix computation for bit and int matrices

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Introduce parallel distance matrix generation using `ndarray` and `rayon` for both `BitMatrix` and `IntMatrix`. Adds full and additive-partial variants for Jaccard, Hamming, Bray-Curtis, Euclidean, and Hellinger metrics. Includes comprehensive unit tests verifying matrix symmetry, zero diagonals, and numerical correctness against pairwise calculations.
This commit is contained in:
Eric Coissac
2026-05-15 17:18:02 +08:00
parent 1881e98bad
commit 8bee9f3017
6 changed files with 488 additions and 0 deletions
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src/Cargo.lock
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@@ -1460,6 +1460,16 @@ dependencies = [
"regex-automata",
]
[[package]]
name = "matrixmultiply"
version = "0.3.10"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "a06de3016e9fae57a36fd14dba131fccf49f74b40b7fbdb472f96e361ec71a08"
dependencies = [
"autocfg",
"rawpointer",
]
[[package]]
name = "mem_dbg"
version = "0.3.4"
@@ -1546,6 +1556,21 @@ version = "0.6.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "729eb334247daa1803e0a094d0a5c55711b85571179f5ec6e53eccfdf7008958"
[[package]]
name = "ndarray"
version = "0.16.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "882ed72dce9365842bf196bdeedf5055305f11fc8c03dee7bb0194a6cad34841"
dependencies = [
"matrixmultiply",
"num-complex",
"num-integer",
"num-traits",
"portable-atomic",
"portable-atomic-util",
"rawpointer",
]
[[package]]
name = "niffler"
version = "2.7.0"
@@ -1646,6 +1671,15 @@ dependencies = [
"itoa",
]
[[package]]
name = "num-integer"
version = "0.1.46"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "7969661fd2958a5cb096e56c8e1ad0444ac2bbcd0061bd28660485a44879858f"
dependencies = [
"num-traits",
]
[[package]]
name = "num-traits"
version = "0.2.19"
@@ -1660,6 +1694,8 @@ name = "obicompactvec"
version = "0.1.0"
dependencies = [
"memmap2",
"ndarray",
"rayon",
"tempfile",
]
@@ -2226,6 +2262,12 @@ dependencies = [
"getrandom 0.3.4",
]
[[package]]
name = "rawpointer"
version = "0.2.1"
source = "registry+https://github.com/rust-lang/crates.io-index"
checksum = "60a357793950651c4ed0f3f52338f53b2f809f32d83a07f72909fa13e4c6c1e3"
[[package]]
name = "rayon"
version = "1.12.0"